similar to: dgamma in jags within r

Hello, In WinBUGS 1.4 manual (http://www.mrc-bsu.cam.ac.uk/bugs/winbugs/manual14.pdf), the gamma density is presented as dgamma(r,mu) where r and mu are the shape and rate parameters, respectively. In JAGS (rjags) manual version 1.0.2, May 9, 2008 (http://www-fis.iarc.fr/~martyn/software/jags/jags_user_manual.pdf), on page 26 the gamma density is presented as dgamma(mu,r) instead of dgamma(r,mu).

There is a thread on this topic already: http://finzi.psych.upenn.edu/Rhelp10/2010-August/250934.html I'm rather mystified by a similar problem and wondering whether I've overlooked something obvious. I'm running with latest versions of R and all packages, and latest version of JAGS running under Windows 7. Here's the problem. I have some source code. It's given below -

i am having problem running my own data. yesterday it was working just fine. today it is not. this is the code i was using as an example to follow. this code ALSO worked just fine yesterday, and is no longer working at all. i suspect it is a problem with either my computer or the software, at this point. if THIS won't even run.... something is wrong. i can assure you this isn't

Hi, All, I am getting some funny results trying to use R's built in distribution functions. In R: > dgamma(4.775972,1.37697964405418, 0.106516604930466) [1] 0.05585295 > dgamma(4.775972,1.37697964405418, 0.106516604930466,TRUE) ### THIS IS JUST WRONG! [1] 0.01710129 > log(dgamma(4.775972,1.37697964405418, 0.106516604930466)) [1] -2.885033 > In C:

Hi All, Here 's what I got using dgamma function : > nu<-.2 > nu*log(nu)-log(gamma(nu))+(nu-1)*log(1)-nu*(1) [1] -2.045951 > dgamma(1,nu,nu,1) [1] 0.0801333 > dgamma(1,nu,nu,0) [1] NaN Warning message: NaNs produced in: dgamma(x, shape, scale, log) Could anyone tell me what is wrong here ? I am using R-2.4.1 on windows XP. Thanks a lot.

Anyone used jags.parallel in latest version of R2jags? Ubuntu Oneiric, just ran updates in R to get latest R2jags package which supposedly has added jags.parallel command to send chains to multiple cores ... but when I submit, I get: test <- jags.parallel(d, inits, param, model.file="rats.bug", n.chains=3, n.iter=2000) Error: could not find function

Dear R-Devel group, My name is Alexey, a data scientist from Moscow, currently working for Align Technology Inc. We have recently had a discussion of the results that the dgamma function (stats) returns for an extreme point (x == 0). <dgamma(0,1,1,log = FALSE) [1] 1 and <dgamma(0,0.5,1,log = FALSE) [1] Inf Density appears to be defined in point zero for the distribution with the

Dear all, I have a question regarding using JAGS and R. My problem is that every single time I want to call JAGS from R the latter crashes (i.e. it turns pale and the Windows tells me "R has stopped working". Strangely, if there is a mistake in my jags code, this will be reported without a crash. Only when the code is right and the model should start to run, R stops working. I already

Hello, I can`t figure out how to include a text file for use in an example in the .Rd help files of an R package I am writing. I want the examples section of one help file to look like this: \examples{ # Load the JAGS model mod <- jags.model("model.txt") } The function jags.model tries to read in the file model.txt. So far every time I run R CMD check, I get an error message:

Hallo! I want to use the package bayesmix. Trying the examples I had no success. The reason is, I think: > haveJAGS() [1] FALSE Have read of JAGS executable (I could not find JAGS.exe in my R directory). What is JAGS? Where can I find or download it? Karl

Has anybody had issues running MCMC (either BUGS or JAGS) on data sets of this magnitude (ie 30k x 20-30). I've been trying to run a hierarchical random effects model on expression data but R completely stalls out on jobs run on 32bit R on our server (doesn't respond...then eventually crashes out with an exception fault). Would using 64bit R help with JAGS? (As far as I know there's

May I request that Dirk's package for jags be added to the CRAN archives for Debian and Ubuntu? Installing the rjags package for R requires specific versions of jags to be present on the system. The current version of rjags requires jags version 2.2.0 or later but the version on the Ubuntu archives at Canonical (i.e. not the CRAN archives) is 2.1.0-2 I can always install Dirk's package

Hi, all: I met "Non-conforming parameters for function %*%" problem, when I run the Jags model in R. My model is like this: model{ for(i in 1:n){ for(j in 1:t[i]){ et[i,j]<-yt[i,j]-beta0+betax*xt[i,j]+betat*t[i,j] } for(a in 1:t[i]){ for(b in 1:t[i]){ sigma[i,a,b]<-pow(rho0,abs(t[a]-t[b])) } } phi[i]<-

Can someone explain to me in what way the new (dpqr)gamma parameter can be interpreted as a rate (when shape != 1)? The only gamma rate that I am aware of is the hazard rate given by dgamma/(1-pgamma), the log of which is returned by my hgamma function (event library). Jim -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read

Could anyone give me some clues as to the best way to debug this error message? I think it is from the passing of variables back to R from the jags function which does Bayesian fitting. The curious part for me is that the error messages seem random, yet the input data are always the same. Any suggestions most welcome. Thanks J Compiling model graph Resolving undeclared variables

Hi all I have a couple of obscure questions for R/Splus experts (which unfortunately isn't me!) I am trying to compute Bayes Factors using some Splus code of Raftery in Gilks et al (1996). Only problem is 1) R doesn't seem to have a robust covariance (cov.mve) which I suspect I need rather than a non-robust classical estimate 2) Splus has cov.mve BUT dgamma in Splus doesn't have a

There's an apparent inconsistency between the behavior of d(pqr)gamma and other distribution functions for "bad" parameter values. Specifically, most distributions give NaN and a warning for bad parameters (e.g. probabilities <0 or >1). In contrast, d(pqr)gamma actually gives an error and stops when shape<0. I don't see why it has to be this way -- the internal C code

Hi, In src/nmath/dgamma.c the comment at the top says * DESCRIPTION * * Computes the density of the gamma distribution, * * 1/s (x/s)^{a-1} exp(-x/s) * p(x;a,s) = ----------------------- * (a-1)! * * where `s' is the scale (= 1/lambda in other parametrizations) * and `a' is the shape parameter ( = alpha in

Hi, I am getting the following error when I'm running jags.model() > meas1 <- jags.model(file="measurement.bug",data=dat.test) syntax error, unexpected '}', expecting ',' or ')' Error in jags.model(file = "measurement.bug", data = dat.test) : Parse error on line 1 Below is my JAGS model. Please cc me as I'm a digest subscriber if

Frank (or anyone else), can you offer any comments comparing runjags, R2jags, rjags ? I couldn't find any vignettes, nothing except a brief mention on Task Views. Kevin On Wed, Oct 7, 2009 at 7:48 AM, Frank E Harrell Jr <f.harrell@vanderbilt.edu > wrote: > Have you tried the rjags package which uses the jags system? It is much > more integrated into R and works quite well.